gghic

Phasing and scaffolding polyploid genomes based on Pore-C or Hi-C. https://wangyibin.github.io/CPhasing

Blazing fast toolkit to work with .hic and .cool files

Python bindings for hictk: read and write .cool and .hic files directly from Python

R bindings for hictk: read .cool and .hic files directly from R

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.

Extract Sequence from Genome According to Annotation File

A Nextflow DSL2 pipeline for pretext generation in curation

Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

a Snakemake version of distiller - the Open2C Hi-C mapping workflow

3DGB is a workflow to build 3D models of genomes from HiC data

High-performance stochastic modeling of DNA loop extrusion interactions

Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.

Configurable Hi-C pipeline that is easy to use

Projects realized during Computational Genomics course.

Interactive visualizer ad manual scaffolder of Hi-C contact maps. All-in-one Java-based implementation.

SALSA: A tool to scaffold long read assemblies with Hi-C data

Hi-C Architect for Neural Networks

This repository is about Referring Expression Comprehension Based Visual Question Answering.